The popping noise in the videos.... is that the backfire?

This maybe a dumb question... but what is... what causes a backfire?
I thought it was normally like an obscene bang coming from the exhaust... like a gunshot.

Does the noise happen at any speed/rpm or only at WOT or when you come down from WOT?

if im not mistaken a backfire is caused when detonation occurs too late. causing part of the explosion to come out the exhaust(or somethin like that) ive seen flames shoot out the exhaust on certain backfire occasions(not on the Bonneville).

Actually, backfiring usually occurs when unburned gasoline vapors ignites in the exhaust pipe. This is indicated by a loud bang. Sometimes a flame will come out the tail pipe.

If a car is backfiring.... does it happen at random (at any rpm).... or only at (or after) WOT?

Depends on what'* broken. A bad spring could make it occur more under load.